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Nitrate is a nutrient and signal that regulates gene expression. The nitrate response has been extensively characterized at the organism, organ, and cell-type-specific levels, but intracellular mRNA dynamics remain unexplored. To characterize nuclear and cytoplasmic transcriptome dynamics in response to nitrate, we performed a time-course expression analysis after nitrate treatment in isolated nuclei, cytoplasm, and whole roots. We identified 402 differentially localized transcripts (DLTs) in response to nitrate treatment. Induced DLT genes showed rapid and transient recruitment of the RNA polymerase II, together with an increase in the mRNA turnover rates. DLTs code for genes involved in metabolic processes, localization, and response to stimulus indicating DLTs include genes with relevant functions for the nitrate response that have not been previously identified. Using single-molecule RNA FISH, we observed early nuclear accumulation of the NITRATE REDUCTASE 1 (NIA1) transcripts in their transcription sites. We found that transcription of NIA1, a gene showing delayed cytoplasmic accumulation, is rapidly and transiently activated; however, its transcripts become unstable when they reach the cytoplasm. Our study reveals the dynamic localization of mRNAs between the nucleus and cytoplasm as an emerging feature in the temporal control of gene expression in response to nitrate treatment in Arabidopsis roots.
Assuntos
Arabidopsis , Núcleo Celular , Citoplasma , Regulação da Expressão Gênica de Plantas , Nitratos , Raízes de Plantas , RNA Mensageiro , Arabidopsis/genética , Arabidopsis/metabolismo , Nitratos/metabolismo , Nitratos/farmacologia , Raízes de Plantas/metabolismo , Raízes de Plantas/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Núcleo Celular/metabolismo , Citoplasma/metabolismo , Regulação da Expressão Gênica de Plantas/efeitos dos fármacos , Proteínas de Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Nitrato Redutase/metabolismo , Nitrato Redutase/genéticaRESUMO
The best ideotypes are under mounting pressure due to increased aridity. Understanding the conserved molecular mechanisms that evolve in wild plants adapted to harsh environments is crucial in developing new strategies for agriculture. Yet our knowledge of such mechanisms in wild species is scant. We performed metabolic pathway reconstruction using transcriptome information from 32 Atacama and phylogenetically related species that do not live in Atacama (sister species). We analyzed reaction enrichment to understand the commonalities and differences of Atacama plants. To gain insights into the mechanisms that ensure survival, we compared expressed gene isoform numbers and gene expression patterns between the annotated biochemical reactions from 32 Atacama and sister species. We found biochemical convergences characterized by reactions enriched in at least 50% of the Atacama species, pointing to potential advantages against drought and nitrogen starvation, for instance. These findings suggest that the adaptation in the Atacama Desert may result in part from shared genetic legacies governing the expression of key metabolic pathways to face harsh conditions. Enriched reactions corresponded to ubiquitous compounds common to extreme and agronomic species and were congruent with our previous metabolomic analyses. Convergent adaptive traits offer promising candidates for improving abiotic stress resilience in crop species.
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Clima Desértico , Filogenia , Transcriptoma , Chile , Adaptação Fisiológica , Redes e Vias MetabólicasRESUMO
Despite significant progress in the development of phototherapy drugs, it is widely recognized that natural products remain the primary source of new photoactive compounds. Exploring uncharted flora in the east-central region of Argentina may offer a vast array of opportunities to isolate new photoactive molecules or plant extracts with high potential for use in antimicrobial photodynamic therapy (aPDT) against Candida albicans. To assess the photofungicidal potential of T. sinuata ("contrayerba") against C. albicans, the extracts underwent spectroscopic and chromatographic analysis, resulting in the identification of furanocoumarin metabolites with similar spectrophotometric properties in all extracts. The extract profiles were created using UHPLC-DAD, and seven furanocoumarins (FCs) were detected. The highest photoinactivation against C. albicans was observed for dicholormethanic extracts (MFC = 62.5 µg/mL), equal to xanthotoxin employed as a positive control. Furthermore, we determine that photochemical mechanisms dependent on oxygen (type I and type II processes) and mechanisms independent of oxygen (photoadduct formation) are involved in the death of these yeasts. These results support the use of native plants of the east-central region of Argentina as potent sensitizers for aPDT and suggest that they can replace xanthotoxin in treating superficial yeast infections of the skin.
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For comprehensive gene expression analyses of the phytopathogenic fungus Botrytis cinerea, which infects a number of plant taxa and is a cause of substantial agricultural losses worldwide, we developed BEB, a web-based B. cinerea gene Expression Browser. This computationally inexpensive web-based application and its associated database contain manually curated RNA-Seq data for B. cinerea. BEB enables expression analyses of genes of interest under different culture conditions by providing publication-ready heatmaps depicting transcript levels, without requiring advanced computational skills. BEB also provides details of each experiment and user-defined gene expression clustering and visualization options. If needed, tables of gene expression values can be downloaded for further exploration, including, for instance, the determination of differentially expressed genes. The BEB implementation is based on open-source computational technologies that can be deployed for other organisms. In this case, the new implementation will be limited only by the number of transcriptomic experiments that are incorporated into the platform. To demonstrate the usability and value of BEB, we analyzed gene expression patterns across different conditions, with a focus on secondary metabolite gene clusters, chromosome-wide gene expression, previously described virulence factors, and reference genes, providing the first comprehensive expression overview of these groups of genes in this relevant fungal phytopathogen. We expect this tool to be broadly useful in B. cinerea research, providing a basis for comparative transcriptomics and candidate gene identification for functional assays.
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Nitrate is a nutrient and a potent signal that impacts global gene expression in plants. However, the regulatory factors controlling temporal and cell type-specific nitrate responses remain largely unknown. We assayed nitrate-responsive transcriptome changes in five major root cell types of the Arabidopsis thaliana root as a function of time. We found that gene-expression response to nitrate is dynamic and highly localized and predicted cell type-specific transcription factor (TF)-target interactions. Among cell types, the endodermis stands out as having the largest and most connected nitrate-regulatory gene network. ABF2 and ABF3 are major hubs for transcriptional responses in the endodermis cell layer. We experimentally validated TF-target interactions for ABF2 and ABF3 by chromatin immunoprecipitation followed by sequencing and a cell-based system to detect TF regulation genome-wide. Validated targets of ABF2 and ABF3 account for more than 50% of the nitrate-responsive transcriptome in the endodermis. Moreover, ABF2 and ABF3 are involved in nitrate-induced lateral root growth. Our approach offers an unprecedented spatiotemporal resolution of the root response to nitrate and identifies important components of cell-specific gene regulatory networks.
Assuntos
Proteínas de Arabidopsis/genética , Fatores de Transcrição de Zíper de Leucina Básica/genética , Proteínas de Ligação a DNA/genética , Regulação da Expressão Gênica de Plantas , Nitratos/metabolismo , Fenômenos Fisiológicos Vegetais , Fatores de Transcrição/genética , Arabidopsis/fisiologia , Proteínas de Arabidopsis/metabolismo , Fatores de Transcrição de Zíper de Leucina Básica/metabolismo , Biologia Computacional/métodos , Proteínas de Ligação a DNA/metabolismo , Perfilação da Expressão Gênica , Ontologia Genética , Redes Reguladoras de Genes , Modelos Biológicos , Especificidade de Órgãos/genética , Raízes de Plantas/fisiologia , Fatores de Transcrição/metabolismo , TranscriptomaRESUMO
RESUMEN Introducción: La enfermedad arterial coronaria ha experimentado un aumento entre los angolanos debido a la transición epidemiológica resultante de los nuevos estilos de vidas desfavorables para la salud cardiovascular. Objetivo: Realizar una caracterización clínico-angiográfica de los pacientes con sospecha de enfermedad arterial coronaria llevados a coronariografía. Método: Estudio observacional retrospectivo, realizado en la Clínica Girassol, con 450 pacientes llevados a coronariografía durante enero del 2012 a diciembre del 2018. Se incluyeron variables clínicas (sexo, edad, tipo de procedimiento, factores de riesgo, indicación clínica) y angiográficas (vía de acceso, vasos afectados, dominancia coronaria, estrategia de tratamiento y complicaciones). Resultados: Predominó el sexo masculino (71,6%) con edad media de 59,7(11,2 años. La hipertensión arterial fue el factor de riesgo predominante (76,0%). El 56,2% de los procedimientos fueron realizados de urgencia siendo el síndrome coronario agudo con elevación del ST (37,3%) el más frecuente. La mayoría de los procedimientos (81,1%) fueron por vía femoral. La descendente anterior estuvo afectada en el 37,6% de los casos y la dominancia derecha fue la más prevalente (94,0%). El hematoma femoral constituyó la complicación más frecuente (0,9%). Conclusiones: En los pacientes intervenidos predominó el sexo masculino, las edades avanzadas, la hipertensión arterial y la realización urgente del procedimiento, mayoritariamente por síndromes coronarios agudos con elevación del segmento ST, con muy baja incidencia de complicaciones.
ABSTRACT Introduction: Coronary artery disease has progressively increased among Angolans due to the epidemiological transition resulting from new lifestyles unfavorable to cardiovascular health. Objective: To perform a clinical-angiographic characterization of patients suspected of coronary artery disease undergoing coronary angiography. Method: Retrospective observational study, conducted at Clínica Girassol, with 450 patients who underwent coronary angiography from January 2012 to December 2018. Clinical variables such as sex, age, type of procedure, risk factors, clinical indication, and angiographic features (access route, vessels involved, coronary dominance, treatment strategy and complications) were included. Results: Male sex predominated (71.6%) with a mean age of 59.7±11.2 years. Hypertension was the predominant risk factor (76.0%). Emergency procedures accounted for 56.2% of the interventions; ST-segment elevation acute coronary syndrome (37.3%) was the most frequent. Most of the procedures (81.1%) were performed via the femoral artery. The left anterior descending artery was involved in 37.6% of the cases and right dominance was the most prevalent (94.0%). Femoral hematoma was the most frequent complication (0.9%). Conclusions: The patients who underwent surgery were predominantly male, older, hypertensive, and required urgent procedures, mostly for ST-segment elevation acute coronary syndromes, with very low rates of complications.
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Fatores de Risco , Síndrome Coronariana AgudaRESUMO
Chromatin accessibility is directly linked with transcription in eukaryotes. Accessible regions associated with regulatory proteins are highly sensitive to DNase I digestion and are termed DNase I hypersensitive sites (DHSs). DHSs can be identified by DNase I digestion, followed by high-throughput DNA sequencing (DNase-seq). The single-base-pair resolution digestion patterns from DNase-seq allows identifying transcription factor (TF) footprints of local DNA protection that predict TF-DNA binding. The identification of differential footprinting between two conditions allows mapping relevant TF regulatory interactions. Here, we provide step-by-step instructions to build gene regulatory networks from DNase-seq data. Our pipeline includes steps for DHSs calling, identification of differential TF footprints between treatment and control conditions, and construction of gene regulatory networks. Even though the data we used in this example was obtained from Arabidopsis thaliana, the workflow developed in this guide can be adapted to work with DNase-seq data from any organism with a sequenced genome.
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Cromatina/metabolismo , Mapeamento Cromossômico/métodos , Pegada de DNA/métodos , Desoxirribonuclease I/metabolismo , Regulação da Expressão Gênica/genética , Redes Reguladoras de Genes/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Arabidopsis/genética , Arabidopsis/metabolismo , Cromatina/genética , Genômica , Ligação Proteica , Software , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismoRESUMO
Plants possess a robust metabolic network for sensing and controlling reactive oxygen species (ROS) levels upon stress conditions. Evidence shown here supports a role for TGA class II transcription factors as critical regulators of genes controlling ROS levels in the tolerance response to UV-B stress in Arabidopsis. First, tga256 mutant plants showed reduced capacity to scavenge H2O2 and restrict oxidative damage in response to UV-B, and also to methylviologen-induced photooxidative stress. The TGA2 transgene (tga256/TGA2 plants) complemented these phenotypes. Second, RNAseq followed by clustering and Gene Ontology term analyses indicate that TGA2/5/6 positively control the UV-B-induced expression of a group of genes with oxidoreductase, glutathione transferase, and glucosyltransferase activities, such as members of the glutathione S-transferase Tau subfamily (GSTU), which encodes peroxide-scavenging enzymes. Accordingly, increased glutathione peroxidase activity triggered by UV-B was impaired in tga256 mutants. Third, the function of TGA2/5/6 as transcriptional activators of GSTU genes in the UV-B response was confirmed for GSTU7, GSTU8, and GSTU25, using quantitative reverse transcription-PCR and ChIP analyses. Fourth, expression of the GSTU7 transgene complemented the UV-B-susceptible phenotype of tga256 mutant plants. Together, this evidence indicates that TGA2/5/6 factors are key regulators of the antioxidant/detoxifying response to an abiotic stress such as UV-B light overexposure.
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Proteínas de Arabidopsis , Arabidopsis , Estresse Oxidativo , Fatores de Transcrição , Raios Ultravioleta , Arabidopsis/genética , Arabidopsis/metabolismo , Arabidopsis/efeitos da radiação , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Regulação da Expressão Gênica de Plantas , Peróxido de Hidrogênio/metabolismo , Espécies Reativas de Oxigênio/metabolismo , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismoRESUMO
Bats are among the most diverse, widespread, and abundant mammals. In Argentina, 67 species of bats have been recorded, belonging to 5 families and 29 genera. These high levels of biodiversity are likely to complicate identification at fieldwork, especially between closely related species, where external morphology-based approaches are the only immediate means for a priori species assignment. The use of molecular markers can enhance species identification, and acquires particular relevance in capture-release studies. In this study, we discuss the extent of the use of the mitochondrial cytochrome b gene for species identification, comparing external morphology identification with a molecular phylogenetic classification based on this marker, under the light of current bat systematics. We analyzed 33 samples collected in an eco-epidemiological survey in the province of Santa Fe (Argentina). We further sequenced 27 museum vouchers to test the accuracy of cytochrome b -based phylogenies in taxonomic identification of bats occurring in the Pampean/Chacoan regions of Argentina. The cytochrome b gene was successfully amplified in all Molossid and Vespertilionid species except for Eptesicus, for which we designed a new reverse primer. The resulting Bayesian phylogeny was congruent with current systematics. Cytochrome b proved useful for species-level delimitation in non-conflicting genera (Eumops, Dasypterus, Molossops) and has infrageneric resolution in more complex lineages (Eptesicus, Myotis, Molossus). We discuss four sources of incongruence that may act separately or in combination: 1) molecular processes, 2) biology, 3) limitations in identification, and 4) errors in the current taxonomy. The present study confirms the general applicability of cytochrome b -based phylogenies in eco-epidemiological studies, but its resolution and reliability depend mainly, but not solely, on the level of genetic differentiation within each bat genus.
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Quirópteros/genética , Citocromos b/genética , DNA Mitocondrial/genética , Variação Genética , Animais , Argentina , FilogeniaRESUMO
RESUMEN Un corazón con tres aurículas, que sumaba cinco cámaras en total, fue un hecho que sorprendió a la medicina hace ya más de un siglo. Este raro defecto cardíaco congénito tiene muy baja incidencia, lo cual hace que sea muy poco conocido por las jóvenes generaciones de médicos dedicados a las enfermedades cardiovasculares. El cor triatriatum sinister generalmente se diagnostica en la temprana infancia y es considerado una causa congénita de estenosis mitral. La conducta quirúrgica es de elección para poder liberar el obstáculo al adecuado flujo sanguíneo a través de la aurícula izquierda. Se presenta el caso de un adulto joven con síntomas típicos de estenosis mitral, sin aparentes elementos claves al examen físico y con un ecocardiograma que evidencia esta anomalía, apenas vista y publicada en nuestro medio en pacientes adultos.
ABSTRACT A heart with three atria, totaling five chambers in all, was a fact that surprised medicine more than a century ago. This rare congenital heart defect has a very low incidence, which makes it very little known to the young generations of doctors dedicated to cardiovascular diseases. The cor triatriatum sinister is usually diagnosed in early childhood, and it is considered a congenital cause of mitral stenosis. Surgical approach is the choice to release the obstacle in order to adequate blood flow through the left atrium. We present the case of a young adult with typical symptoms of mitral stenosis, without apparent key elements on the physical examination and that the echocardiogram showed this anomaly, hardly seen and published in our field in adult patients.
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Coração Triatriado , Função do Átrio Esquerdo , Defeitos dos Septos Cardíacos , Estenose da Valva MitralRESUMO
Cholesterol Gallstone Disease (GSD) is a common multifactorial disorder characterized by crystallization and aggregation of biliary cholesterol in the gallbladder. The global prevalence of GSD is ~10-20% in the adult population but rises to 28% in Chile (17% among men and 30% among women). The small intestine may play a role in GSD pathogenesis, but the molecular mechanisms have not been clarified. Our aim was to identify the role of the small intestine in GSD pathogenesis. Duodenal biopsy samples were obtained from patients with GSD and healthy volunteers. GSD status was defined by abdominal ultrasonography. We performed a transcriptome study in a discovery cohort using Illumina HiSeq. 2500, and qPCR, immunohistochemistry and immunofluorescence were used to validate differentially expressed genes among additional case-control cohorts. 548 differentially expressed genes between GSD and control subjects were identified. Enriched biological processes related to cellular response to zinc, and immune and antimicrobial responses were observed in GSD patients. We validated lower transcript levels of metallothionein, NPC1L1 and tight junction genes and higher transcript levels of genes involved in immune and antimicrobial pathways in GSD patients. Interestingly, serum zinc and phytosterol to cholesterol precursor ratios were lower in GSD patients. A significant association was observed between serum zinc and phytosterol levels. Our results support a model where proximal small intestine plays a key role in GSD pathogenesis. Zinc supplementation, modulation of proximal microbiota and/or intestinal barrier may be novel targets for strategies to prevent GSD.
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Colelitíase/metabolismo , Colesterol/metabolismo , Duodeno/metabolismo , Inflamação/metabolismo , Junções Íntimas/metabolismo , Zinco/metabolismo , Adulto , Biópsia , Colelitíase/diagnóstico por imagem , Colelitíase/patologia , Feminino , Regulação da Expressão Gênica , Humanos , Masculino , Proteínas de Membrana Transportadoras/metabolismo , Metalotioneína/metabolismo , Microbiota , Prevalência , RNA-Seq , Fatores de Risco , Proteínas de Junções Íntimas/metabolismo , Transcriptoma , Ultrassonografia , Adulto JovemRESUMO
In avian species living at high altitudes and latitudes, reproductive events are largely controlled by photoperiod, with changes being perceived mainly through encephalic photoreceptors located in the hypothalamus. It is known that during long day periods (reproductive periods), the information transmitted by brain photoreceptors triggers the production of thyroid hormones that regulate GnRH secretion, inducing secretion of pituitary gonadotropins. As a result, gonads develop and grow and the production of gonadal sex hormones, testosterone and estradiol increases (classic gonadal cycle). During short day periods (non-reproductive periods) on the other hand, the gonads regress, and plasma gonadal steroid levels are low. By means of this mechanism, birds synchronize their physiology and reproductive behaviors with seasonal changes in the environment. However, it appears that not all avian species comply with this general reproductive pattern. For example, the Eared Dove (Zenaida auriculata), a South American opportunistic breeding columbiform, has been reported to successfully reproduce throughout the year, making it an interesting avian system for studying the endocrine basis of avian reproduction. In view of a clear lack of seasonal variability in testicular weight and size (the classic gonadal regression/recrudescence cycle) in the male Eared Dove, we examined whether their reproductive aseasonality could be the result of being in a continuous state of reproductive preparedness. Our results show that despite the absence of a marked gonadal cycle in terms of gonadal volume, plasma testosterone levels in males were minimal during autumn-winter, reaching maximum values during spring-summer. This indicates that male gonad function is not seasonal in terms of spermatogenesis but that circulating testosterone levels are correlated with photoperiod, demonstrating an exception to the classic model of reproduction in birds.
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Columbidae/fisiologia , Reprodução/fisiologia , Estações do Ano , Animais , Columbidae/sangue , Masculino , Testosterona/sangueRESUMO
Transcriptional regulation, determined by the chromatin structure and regulatory elements interacting at promoter regions, is a key step in plant responses to environmental cues. Nitrate (NO3-) is a nutrient signal that regulates the expression of hundreds of genes in Arabidopsis thaliana. Here, we integrate mRNA sequencing, genome-wide RNA polymerase II (RNPII), chromatin immunoprecipitation sequencing, and DNase sequencing datasets to establish the relationship between RNPII occupancy and chromatin accessibility in response to NO3- treatments in Arabidopsis roots. Genomic footprinting allowed us to identify in vivo regulatory elements controlling gene expression in response to NO3- treatments. NO3--modulated transcription factor (TF) footprints are important for a rapid increase in RNPII occupancy and transcript accumulation over time. We mapped key TF regulatory interactions and functionally validated the role of NAP, an NAC-domain containing TF, as a new regulatory factor in NO3- transport. Taken together, our study provides a comprehensive view of transcriptional networks in response to a nutrient signal in Arabidopsis roots.
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Arabidopsis/efeitos dos fármacos , Arabidopsis/genética , Cromatina/genética , Redes Reguladoras de Genes/efeitos dos fármacos , Nitratos/farmacologia , Raízes de Plantas/efeitos dos fármacos , Raízes de Plantas/genética , Arabidopsis/metabolismo , Proteínas de Arabidopsis/metabolismo , Transporte Biológico , Cromatina/efeitos dos fármacos , Cinética , Nitratos/metabolismo , RNA Polimerase II/metabolismo , RNA Mensageiro/genética , Proteínas Repressoras/metabolismo , Fatores de Transcrição/metabolismoRESUMO
Glioblastoma multiforme is considered to be one of the most aggressive types of tumors of the central nervous system, with a poor prognosis and short survival periods of ~ one year. The current protocol for glioblastoma treatment includes the surgical excision of the primary tumor followed by radio and chemotherapy. Photodynamic therapy (PDT) is considered a promising strategy for the treatment of several types of tumors. Phthalocyanines (Pcs) are good photosensitizers (PSs) for PDT because they induce cell death in several cellular models. ZnPc (Zn(II)phthalocyanine) is a well-known Pc, extensively tested in different cells and tumor models, but its evaluation on a glioblastoma model has been poorly studied. Herein, we compare the capacity of ZnPc and one of its derivatives, Zn(II)tetraminephthalocyanine (TAZnPc), to photoinactivate glioblastoma cells (T98G, MO59, LN229 and U87-MG) in culture. We measured the cellular uptake, the toxicity in the dark and the subcellular localization of the different Pcs, as well as the clonogenic capacity of surviving cells after PDT. The mechanism of cell death induced after PDT was determined by measuring caspase 3 activation, DNA fragmentation, phosphatidylserine externalization, mitochondrial morphological changes and loss of mitochondrial membrane potential as well as lysosomal membrane integrity. Overall, ZnPc and TAZnPc present good properties to be used as PSs with photoinactivation capacity on glioblastoma cells.
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Glioblastoma/tratamento farmacológico , Indóis/toxicidade , Compostos Organometálicos/toxicidade , Fotoquimioterapia/métodos , Fármacos Fotossensibilizantes/toxicidade , Caspase 3/metabolismo , Linhagem Celular Tumoral , Fragmentação do DNA , Humanos , Indóis/química , Indóis/farmacologia , Isoindóis , Lisossomos/efeitos dos fármacos , Mitocôndrias/efeitos dos fármacos , Compostos Organometálicos/química , Compostos Organometálicos/farmacologia , Fármacos Fotossensibilizantes/química , Fármacos Fotossensibilizantes/farmacologia , Compostos de ZincoRESUMO
Whole human genome sequencing initiatives help us understand population history and the basis of genetic diseases. Current data mostly focuses on Old World populations, and the information of the genomic structure of Native Americans, especially those from the Southern Cone is scant. Here we present annotation and variant discovery from high-quality complete genome sequences of a cohort of 11 Mapuche-Huilliche individuals (HUI) from Southern Chile. We found approximately 3.1 × 106 single nucleotide variants (SNVs) per individual and identified 403,383 (6.9%) of novel SNVs events. Analyses of large-scale genomic events detected 680 copy number variants (CNVs) and 4,514 structural variants (SVs), including 398 and 1,910 novel events, respectively. Global ancestry composition of HUI genomes revealed that the cohort represents a sample from a marginally admixed population from the Southern Cone, whose main genetic component derives from Native American ancestors. Additionally, we found that HUI genomes contain variants in genes associated with 5 of the 6 leading causes of noncommunicable diseases in Chile, which may have an impact on the risk of prevalent diseases in Chilean and Amerindian populations. Our data represents a useful resource that can contribute to population-based studies and for the design of early diagnostics or prevention tools for Native and admixed Latin American populations.
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Etnicidade/genética , Marcadores Genéticos , Genética Populacional , Genoma Humano , Genômica/métodos , Polimorfismo de Nucleotídeo Único , Sequenciamento Completo do Genoma/métodos , Adulto , Idoso , Idoso de 80 Anos ou mais , Chile , Estudos de Coortes , Variações do Número de Cópias de DNA , Feminino , Haplótipos , Humanos , Masculino , Pessoa de Meia-Idade , Adulto JovemRESUMO
Studies conducted in rodents subjected to chronic stress and some observations in humans after psychosocial stress, have allowed to establish a link between stress and the susceptibility to many complex diseases, including mood disorders. The studies in rodents have revealed that chronic exposure to stress negatively affects synaptic plasticity by triggering changes in the production of trophic factors, subunit levels of glutamate ionotropic receptors, neuron morphology, and neurogenesis in the adult hippocampus. These modifications may account for the impairment in learning and memory processes observed in chronically stressed animals. It is plausible then, that stress modifies the interplay between signal transduction cascades and gene expression regulation in the hippocampus, therefore leading to altered neuroplasticity and functioning of neural circuits. Considering that miRNAs play an important role in post-transcriptional-regulation of gene expression and participate in several hippocampus-dependent functions; we evaluated the consequences of chronic stress on the expression of miRNAs in dorsal (anterior) portion of the hippocampus, which participates in memory formation in rodents. Here, we show that male rats exposed to daily restraint stress (2.5 h/day) during 7 and 14 days display a differential profile of miRNA levels in dorsal hippocampus and remarkably, we found that some of these miRNAs belong to the miR-379-410 cluster. We confirmed a rise in miR-92a and miR-485 levels after 14 days of stress by qPCR, an effect that was not mimicked by chronic administration of corticosterone (14 days). Our in silico study identified the top-10 biological functions influenced by miR-92a, nine of which were shared with miR-485: Nervous system development and function, Tissue development, Behavior, Embryonic development, Organ development, Organismal development, Organismal survival, Tissue morphology, and Organ morphology. Furthermore, our in silico study provided a landscape of potential miRNA-92a and miR-485 targets, along with relevant canonical pathways related to axonal guidance signaling and cAMP signaling, which may influence the functioning of several neuroplastic substrates in dorsal hippocampus. Additionally, the combined effect of miR-92a and miR-485 on transcription factors, along with histone-modifying enzymes, may have a functional relevance by producing changes in gene regulatory networks that modify the neuroplastic capacity of the adult dorsal hippocampus under stress.
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The rapid increase in the availability of transcriptomics data generated by RNA sequencing represents both a challenge and an opportunity for biologists without bioinformatics training. The challenge is handling, integrating, and interpreting these data sets. The opportunity is to use this information to generate testable hypothesis to understand molecular mechanisms controlling gene expression and biological processes (Fig. 1). A successful strategy to generate tractable hypotheses from transcriptomics data has been to build undirected network graphs based on patterns of gene co-expression. Many examples of new hypothesis derived from network analyses can be found in the literature, spanning different organisms including plants and specific fields such as root developmental biology.In order to make the process of constructing a gene co-expression network more accessible to biologists, here we provide step-by-step instructions using published RNA-seq experimental data obtained from a public database. Similar strategies have been used in previous studies to advance root developmental biology. This guide includes basic instructions for the operation of widely used open source platforms such as Bio-Linux, R, and Cytoscape. Even though the data we used in this example was obtained from Arabidopsis thaliana, the workflow developed in this guide can be easily adapted to work with RNA-seq data from any organism.
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Arabidopsis/genética , Perfilação da Expressão Gênica , Redes Reguladoras de Genes , Sequenciamento de Nucleotídeos em Larga Escala , Análise de Sequência de RNA , Transcriptoma , Biologia Computacional/métodos , Bases de Dados de Ácidos Nucleicos , Perfilação da Expressão Gênica/métodos , Software , Biologia de Sistemas/métodosRESUMO
The worldwide increase in antibiotic resistance has led to search of alternatives anti-microbial therapies such as photodynamic inactivation. The aim of this paper was to evaluate the photodynamic activity in vitro of a neutral and two cationic Zn phthalocyanines. Their photokilling activity was tested on Escherichia coli ATCC 25922 and Klebsiella pneumoniae Carbapenemase (KPC)-producing. After treating bacteria with phthalocyanines, the cultures were irradiated with white light. As a result, the bacteria were inactivated in presence of cationic phthalocyanines. The photoinactivation was dependent of the irradiation time and phthalocyanine concentration. The most effective photosensitizer on KPC-producing was Zinc(II)tetramethyltetrapyridino[2,3-b:2',3'-g:2â³,3â³-l:2â´,3â´-q]porphyrazinium methylsulfate (ZnTM2,3PyPz). After irradiation using the water soluble ZnTM2,3PyPz (3µM) the viability of KPC (30min of irradiation) and E. coli (10min of irradiation) decreased ≈99.995%.
Assuntos
Farmacorresistência Bacteriana Múltipla/efeitos dos fármacos , Inibidores Enzimáticos/farmacologia , Indóis/farmacologia , Compostos Organometálicos/farmacologia , Fármacos Fotossensibilizantes/farmacologia , Zinco/farmacologia , Proteínas de Bactérias/antagonistas & inibidores , Proteínas de Bactérias/metabolismo , Relação Dose-Resposta a Droga , Inibidores Enzimáticos/síntese química , Inibidores Enzimáticos/química , Escherichia coli/efeitos dos fármacos , Escherichia coli/enzimologia , Indóis/química , Isoindóis , Klebsiella pneumoniae/efeitos dos fármacos , Klebsiella pneumoniae/enzimologia , Testes de Sensibilidade Microbiana , Estrutura Molecular , Compostos Organometálicos/síntese química , Compostos Organometálicos/química , Fármacos Fotossensibilizantes/síntese química , Fármacos Fotossensibilizantes/química , Relação Estrutura-Atividade , Zinco/química , beta-Lactamases/metabolismoRESUMO
Nitrogen (N) is one of the main limiting nutrients for plant growth and crop yield. It is well documented that changes in nitrate availability, the main N source found in agricultural soils, influences a myriad of developmental programs and processes including the plant defense response. Indeed, many agronomical reports indicate that the plant N nutritional status influences their ability to respond effectively when challenged by different pathogens. However, the molecular mechanisms involved in N-modulation of plant susceptibility to pathogens are poorly characterized. In this work, we show that Solanum lycopersicum defense response to the necrotrophic fungus Botrytis cinerea is affected by plant N availability, with higher susceptibility in nitrate-limiting conditions. Global gene expression responses of tomato against B. cinerea under contrasting nitrate conditions reveals that plant primary metabolism is affected by the fungal infection regardless of N regimes. This result suggests that differential susceptibility to pathogen attack under contrasting N conditions is not only explained by a metabolic alteration. We used a systems biology approach to identify the transcriptional regulatory network implicated in plant response to the fungus infection under contrasting nitrate conditions. Interestingly, hub genes in this network are known key transcription factors involved in ethylene and jasmonic acid signaling. This result positions these hormones as key integrators of nitrate and defense against B. cinerea in tomato plants. Our results provide insights into potential crosstalk mechanisms between necrotrophic defense response and N status in plants.
RESUMO
Nitrogen is an essential macronutrient for plants and its availability is a key determinant of plant growth and development and crop yield. Besides their nutritional role, N nutrients and metabolites are signals that activate signaling pathways that modulate many plant processes. Because the most abundant inorganic N source for plants in agronomic soils is nitrate, much of the work to understand plant N-signaling has focused on this nutrient. Over the last years, several studies defined a comprehensive catalog of nitrate-responsive genes, involved in nitrate transport, metabolism and a variety of other processes. Despite significant progress in recent years, primarily using Arabidopsis thaliana as a model system, the molecular mechanisms by which nitrate elicits changes in transcript abundance are still not fully understood. Here we highlight recent advancements in identifying key transcription factors and transcriptional mechanisms that orchestrate the gene expression response to changes in nitrate availability in A. thaliana.